[phenixbb] Strong anomalous signal but AutoSol fails

[mohamed noor]

Hi Tom

Just to check that I am on the right track, I have attached below the
output from phenix.anomalous_signal using a single XDS_ASCII.HKL file from
a single crystal. It is one of a few datasets, but based on Xtriage seems
to be the best one.

The space group is P 3(1/2) 2 1. All datasets were collected at the peak
wavelength (fluorescence scan). My initial feeling that there is a strong
signal comes from CORRECT.LP. Aimless and Xtriage. IIRC, the resolution
difference between the optimistic and pessimistic measurability is about
0.3-0.4 A.


Estimation of anomalous signal in a dataset

Estimating B-value for anomalous substructure as    91.2  based on
overall B-value of    75.4 (Note: you can set this with
b_value_anomalous=xx)

Getting scaled data and half-datasets with scale_and_merge
Log file will be: scale.log

Files for half_dataset CC:
['TEMP4/XDS_ASCII_SG150_1800frames_reprocFriedel_0_1.sca']
Files for half_dataset CC:
['TEMP4/XDS_ASCII_SG150_1800frames_reprocFriedel_0_1.sca']
Files for half_dataset CC:
['TEMP4/XDS_ASCII_SG150_1800frames_reprocFriedel_0_1.sca']
Scaled data are in: scaled_data.mtz
Half-dataset A is in: half_dataset_a.mtz
Half-dataset B is in: half_dataset_b.mtz
Using scaled data in analysis


Setting up estimator for CC*

-------------------Summary of signal in this dataset
------------------------

       Shell
                       CCano   Nrefl Nrefl
Resolution Esqr I/sigI  half   anom   half
47.8- 7.0  0.50  19.55  0.32    2389  2360
 7.0- 6.5  0.69  10.63  0.11     621   608
 6.5- 6.0  0.87   8.47  0.08     850   818
 6.0- 5.5  0.88   7.52  0.08    1189  1141
 5.5- 5.0  0.72   5.88  0.09    1709  1588
 5.0- 4.5  0.76   4.59  0.07    2521  2247
 4.5- 4.0  0.98   3.25  0.05    3881  3268
 4.0- 3.5  0.79   3.23  0.24    4001  2577
 3.5- 3.3  1.72   1.99 -0.02    3420  2118

       Cumulative

----------------------Data quality-----------------    Best guess of
expected
                                                      results of finding
sites
                                                     ------ and
phasing--------

                     CCano   Nrefl                    P(Substr)
Resolution Skew Esqr  half   anom    CC* Signal  +/-     (%)       FOM*  +/-
47.8- 7.0  0.02 0.47  0.32    2389  0.51  10.1   1.3      68       0.2   0.0
47.8- 6.5  0.02 0.50  0.28    3010  0.48  10.7   1.7      72       0.2   0.1
47.8- 6.0  0.02 0.57  0.24    3860  0.43  10.8   2.8      72       0.2   0.1
47.8- 5.5  0.05 0.64  0.20    5049  0.44  12.6   2.4      78       0.2   0.1
47.8- 5.0  0.01 0.66  0.17    6758  0.39  12.8   3.3      78       0.2   0.1
47.8- 4.5  0.01 0.69  0.14    9279  0.36  13.4   3.4      82       0.2   0.1
47.8- 4.0  0.00 0.77  0.12   13160  0.33  14.3   3.6      88       0.2   0.1
47.8- 3.5  0.00 0.77  0.15   17161  0.39  18.4   3.8      98       0.3   0.1
47.8- 3.3  0.00 0.88  0.14   20581  0.31  15.7   2.1      95       0.2   0.0


On Fri, Aug 7, 2015 at 2:30 PM, Terwilliger, Thomas Charles <
terwilliger at lanl.gov> wrote:

> Hi Mohamed,
>
> You might try running phenix.anomalous_signal on your data (may require
> finding your unmerged data and running phenix.scale_and_merge first).  This
> will give you an idea if you should be able to solve your SAD dataset.
>
> See:
> http://www.phenix-online.org/version_docs/1.10pre-2124/reference/anomalous_signal.html
>
> All the best,
> Tom T
>
>
>
>
>
> From: phenixbb-bounces at phenix-online.org [
> phenixbb-bounces at phenix-online.org] on behalf of mohamed noor [
> mohamed.noor34 at gmail.com]
>
> Sent: Thursday, August 06, 2015 3:16 PM
>
> To: PHENIX user mailing list
>
> Subject: [phenixbb] Strong anomalous signal but AutoSol fails
>
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> Dear developers
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> I have a low resolution anomalous dataset which Aimless suggests has an
> effective resolution to 3.3 A and anomalous signal to 3.5 A. However, SAD
> phasing with AutoSol is not successful with the final R factor around 50 %.
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> I also have another dataset collected at a remote wavelength without
> anomalous signal to 3 A but they are not isomorphous (> 2 A difference in c
> axis).
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> The anomalous signal comes from the ligand heme c, which is bound
> covalently to the protein, so its occupancy should be 1. The protein is
> quite small with about 120 residues. Xtriage suggests an NCS of 6 to 20
> with most likely number to be 13.
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> Is there any reason why a reasonable solution cannot be found? There is no
> twinning.
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> I am using the latest nightly 1.10 pre2124.
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> Thanks.
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